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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

CLRN1 Gene

protein-coding GIFtS: 52
GCID: GC03M150643

clarin 1

(Previous name: Usher syndrome 3A )
(Previous symbols: USH3, USH3A)

Explore 8 diseases affiliated with
CLRN1 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Clarin 1¹ ²		Usher Syndrome 3A¹
USH3A¹ ² ³ ⁵		RP61²
USH3¹ ² ⁵		Clarin-1¹
Usher Syndrome Type-3 Protein² ³

External Ids:	HGNC: 12605¹	Entrez Gene: 7401²	Ensembl: ENSG00000163646⁷	OMIM: 606397⁵	UniProtKB: P58418³

Export aliases for CLRN1 gene to outside databases

Previous GC identifers: GC03M152127 GC03M148017

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for CLRN1:

This gene encodes a protein that contains a cytosolic N-terminus, multiple helical transmembrane domains, and an

endoplasmic reticulum membrane retention signal, TKGH, in the C-terminus. The encoded protein may be important in

development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher

syndrome type IIIa. Multiple transcript variants encoding distinct isoforms have been identified for this gene.

(provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: CLRN1_HUMAN, P58418

Function: May have a role in the excitatory ribbon synapse junctions between hair cells and cochlear ganglion cells and

presumably also in analogous synapses within the retina

Gene Wiki entry for CLRN1

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000003.11 NC_018914.1 NT_005612.16

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the CLRN1 gene promoter:
ATF-2 FOXO3 Nkx2-5 Tal-1beta LCR-F1 FOXO3b SRY FOXO4 FOXO3a
Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): CLRN1 promoter sequence

Search SABiosciences Chromatin IP Primers for CLRN1

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CLRN1

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3q25 Ensembl cytogenetic band: 3q25.1 HGNC cytogenetic band: 3q21-q25

CLRN1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLRN1 gene location

GeneLoc information about chromosome 3 GeneLoc Exon Structure

GeneLoc location for GC03M150643: view genomic region (about GC identifiers)

Start:	150,643,950 bp from pter	End:	150,690,786 bp from pter
Size:	46,837 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: CLRN1_HUMAN, P58418 (See protein sequence)

Recommended Name: Clarin-1

Size: 232 amino acids; 25719 Da

Subcellular location: Membrane; Multi-pass membrane protein (Potential)

Secondary accessions: D3DNJ3 E1ACU9 Q8N6A9

Alternative splicing: 3 isoforms: P58418-3 P58418-1 P58418-4

Explore the universe of human proteins at neXtProt for CLRN1: NX_P58418

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_P58418

CLRN1 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins (4 alternative transcripts):

NP_001182723.1 NP_001243748.1 NP_443721.1 NP_777367.1

ENSEMBL proteins:

ENSP00000295911 ENSP00000322280 ENSP00000419892 ENSP00000419244 ENSP00000329158

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	Uscn Proteins for CLRN1

Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005886	plasma membrane	IDA	19423712
GO:0005902	microvillus	IDA	19423712
GO:0016021	integral to membrane	IEA	--
GO:0030027	lamellipodium	IDA	19423712

CLRN1 for ontologies About GeneDecksing

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	Uscn ELISAs and CLIAs for CLRN1

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

CLRN1 for domains About GeneDecksing

1 InterPro domain/family:

IPR026748 Clarin

Graphical View of Domain Structure for InterPro Entry P58418

ProtoNet protein and cluster: P58418

UniProtKB/Swiss-Prot: CLRN1_HUMAN, P58418

Similarity: Belongs to the clarin family

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

UniProtKB/Swiss-Prot: CLRN1_HUMAN, P58418

Function: May have a role in the excitatory ribbon synapse junctions between hair cells and cochlear ganglion cells and

presumably also in analogous synapses within the retina

miRNA Products:		Browse 3'-UTR reporter clones for miRNA target validation Browse MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat CLRN1
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		hsa-miR-30c hsa-miR-607 hsa-miR-875-3p hsa-miR-1237 hsa-miR-196a* hsa-miR-3065-5p hsa-miR-488 hsa-miR-30d

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In Situ Assay
Products:

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1 GenomeRNAi human phenotype for CLRN1:

Increased gamma-H2AX phosphory

Animal Models:
Mouse knock-out Clrn1^tm1.1Kuna for CLRN1
5 MGI mutant phenotypes (inferred from 3 alleles) (MGI details for Clrn1):

behavior/neurological

hearing/vestibular/ear

nervous system

no phenotypic analysis

vision/eye

CLRN1 for phenotypes About GeneDecksing

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for CLRN1

Gene Ontology (GO): 5/9 biological process terms (GO ID links to tree view) (see all 9): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0007015	actin filament organization	IDA	19423712
GO:0007605	sensory perception of sound	IMP	15650299
GO:0010592	positive regulation of lamellipodium assembly	IDA	19423712
GO:0045494	photoreceptor cell maintenance	IMP	15521980
GO:0048870	cell motility	IDA	19423712

CLRN1 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for CLRN1
Search CenterWatch for drugs/clinical trials and news about CLRN1

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for CLRN1 gene (5 alternative transcripts):

NM_001195794.1 NM_001256819.1 NM_052995.2 NM_174878.2 NM_174880.1

Unigene Cluster for CLRN1:

Clarin 1

Hs.380222 [show with all ESTs]

Unigene Representative Sequence: NR_046380

6 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000295911(uc003eyj.3) ENST00000327047(uc021xfs.1 uc003eyk.1 uc021xft.1 uc021xfu.1 uc021xfv.1 uc021xfw.1)

ENST00000468836 ENST00000485607 ENST00000472224 ENST00000328863

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		hsa-miR-30c hsa-miR-607 hsa-miR-875-3p hsa-miR-1237 hsa-miR-196a* hsa-miR-3065-5p hsa-miR-488 hsa-miR-30d

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Additional cDNA sequence:

AF388366.1 AF482697.1 AF495717.1 BC074970.2 BC074971.2 HM626132.1 HM626133.1 HM626134.1

HM626135.1 HM626136.1 HM626137.1 HM626138.1 NR_046380.1

3 DOTS entries:

DT.100001565 DT.97825200 DT.97789602

13 AceView cDNA sequences:

AF388368 AF495717 BM666773 NM_052995 BM694985 NM_174878 BC074971 NM_174880

BC074970 AF388366 AF482697 BX491536 W27577

GeneLoc Exon Structure

5 Alternative Splicing Database (ASD) splice patterns (SP) for CLRN1 About this scheme

ExUns:	1a	·	1b	·	1c	^	2a	·	2b	^	3	^	4a	·	4b	·	4c	^	5a	·	5b	^	6
SP1:											-						-				-
SP2:							-		-		-						-
SP3:
SP4:							-				-
SP5:							-		-		-

ECgene alternative splicing isoforms for CLRN1

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

CLRN1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GAATATATTT

About this image

CLRN1 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

1 LifeMap In Vivo Development Anatomical Compartment/Cell

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Eye

Inner Nuclear Layer

Cholinergic Amacrine Cells

Amacrine, Retina

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See CLRN1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for CLRN1

SOURCE GeneReport for Unigene cluster: Hs.380222

UniProtKB/Swiss-Prot: CLRN1_HUMAN, P58418

Tissue specificity: Widely expressed. Found in the retina

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In Situ
Assay Products:

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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of chordates.

Orthologs for CLRN1 gene from 3/12 species (see all 12) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	CLRN1¹	clarin 1	71.26(n) 71.12(a)		771718 XM_001233893.1 XP_001233894.1
lizard (Anolis carolinensis)	Reptilia	CLRN1⁶	--	72(a)	1 ↔ 1	3(18189005-18189274)
zebrafish (Danio rerio)	Actinopterygii	clrn1¹	clarin 1	63.79(n) 60.78(a)		436944 NM_001002671.1 NP_001002671.1

ENSEMBL Gene Tree for CLRN1 (if available)
TreeFam Gene Tree for CLRN1 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for CLRN1 gene

CLRN3² CLRN2²

1 SIMAP similar gene for CLRN1 using alignment to 5 protein entries: CLRN1_HUMAN (see all proteins):

CLRN2

CLRN1 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 3 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs111033422^1,2	C,F,	non-pathogenic	234794164(-)	`ATGCCA/CAGCCA`	7	P	syn¹		4		CSA WA NA EU	5990
rs3796242^1,2	C,F,H,	non-pathogenic	234794215(-)	`TTTGCA/TTGTGC`	7	A	syn¹ ese³		24		EA NA NS WA EU	9851
rs121908143^1,2	C	pathogenic	234794276(-)	`TCCTCT/GGCAAA`	7	/G /C	mis¹		1		NA	4552
rs111033258^1,2	C	pathogenic	234794302(-)	`GTCAAG/TGCCTC`	7	K N	mis¹		0	--	--	--	--
rs111033267^1,2	C	pathogenic	234794347(-)	`CAGTAA/CGGGCT`	7	* Y	stg¹		0	--	--	--	--
rs121908140^1,2	C,	pathogenic	234838890(-)	`ACTTAG/TGTCTA`	8	* Y	stg¹ ut3¹		0	--	--	--	--
rs78068578^1,2	F,	--	148016742(+)	`ACACGT/ACTTGC`	1	--	ds500¹		1		WA	118
rs6764182^1,2	C,F,H,	--	148017468(+)	`CTAGCC/GCACTC`	5	--	ds500¹ ut3¹ ese³		11		NS EA WA NA	724
rs113817098^1,2		--	148017808(+)	`TCAGCG/ACCTGT`	5	--	ut3¹ nc-transcript-variant		1		CSA	2
rs16863066^1,2	C,F,H,	--	148018035(+)	`ATACCG/ATCATA`	5	--	ut3¹ nc-transcript-variantint¹ ese³		12		NA NS EA WA	1334

HapMap Linkage Disequilibrium report for CLRN1 (150643950 - 150690786 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for CLRN1: --
Human Gene Mutation Database (HGMD): CLRN1

Locus Specific Mutation Databases (LSDB): CLRN1

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing CLRN1

DNA2.0 Custom Variant and Variant Library Synthesis for CLRN1

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

CLRN1 for disorders           About GeneDecksing

OMIM gene information: 606397
OMIM disorders: 276902
UniProtKB/Swiss-Prot: CLRN1_HUMAN, P58418

Defects in CLRN1 are the cause of Usher syndrome type 3A (USH3A) [MIM:276902]. USH is a genetically

heterogeneous condition characterized by the association of retinitis pigmentosa and sensorineural deafness. Age at

onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome

type 2 (USH2) and Usher syndrome type 3 (USH3). USH3 is characterized by postlingual progressive deafness and onset of

retinitis pigmentosa in the second decade of life

Defects in CLRN1 are the cause of retinitis pigmentosa type 61 (RP61) [MIM:614180]. RP61 is a retinal

dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment

deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone

photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their

condition progresses, they lose their far peripheral visual field and eventually central vision as well

8 diseases for CLRN1: About MalaCards

usher syndrome usher syndrome type 3 usher syndrome type ii pigmentary retinopathy

retinitis pigmentosa retinitis retinal disease blindness

2 diseases from the University of Copenhagen DISEASES database for CLRN1:

Usher syndrome Retinitis pigmentosa

1 Novoseek disease relationship for CLRN1 gene About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
usher syndrome	94.4	8	15521980 (2), 16545802 (1), 18281613 (1), 12145752 (1) (see all 5)

Human Genome Epidemiology (HuGE) Navigator: CLRN1 (1 document)

Export disorders for CLRN1 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for CLRN1 gene, integrated from 9 sources (see all 30):
(articles sorted by number of sources associating them with CLRN1)

Utopia: connect your pdf to the dynamic
world of online information

Mutation screening of USH3 gene (clarin-1) in Spanish patients with Usher syndrome: low prevalence and phenotypic variability. (PubMed id 15521980)^{1, 2, 9} Aller E.... Millan J.M. (2004)
Usher syndrome type III: revised genomic structure of the USH3 gene and identification of novel mutations. (PubMed id 12145752)^{1, 2, 9} Fields R.R.... Sumegi J. (2002)
CLRN1 mutations cause nonsyndromic retinitis pigmentosa. (PubMed id 21310491)^{1, 2} Khan M.I.... den Hollander A.I. (2011)
Alternative splice variants of the USH3A gene Clarin 1 (CLRN1). (PubMed id 20717163)^{1, 2} Vastinsalo H.... Sankila E.M. (2010)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S....Malek J. (2004)
USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses. (PubMed id 12080385)^{1, 2} Adato A.... Lancet D. (2002)
Mutations in a novel gene with transmembrane domains underlie Usher syndrome type 3. (PubMed id 11524702)^{1, 2} Joensuu T.... Sankila E.-M. (2001)
Refined mapping of the Usher syndrome type III locus on chromosome 3, exclusion of candidate genes, and identification of the putative mouse homologous region. (PubMed id 8975700)^{1, 3} Joensuu T....Sankila E.M. (1996)
Assignment of an Usher syndrome type III (USH3) gene to chromosome 3q. (PubMed id 7711740)^{1, 3} Sankila E.M....de la Chapelle A. (1995)
Disease-causing mutations in the CLRN1 gene alter nor mal CLRN1 protein trafficking to the plasma membrane. (PubMed id 19753315)^{1, 9} Isosomppi J....Sankila E.M. (2009)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Disorders
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 7401	HGNC: 12605	AceView: USH3A	Ensembl:ENSG00000163646	euGenes: HUgn7401
ECgene: CLRN1	H-InvDB: CLRN1

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for CLRN1	Pharmacogenomics, SNPs, Pathways
Mutations of the USH3A gene	http://www.retina-international.org/files/sci-news/ush3mut.htm
GeneReviews	http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CLRN1

Intellectual Property for CLRN1 gene
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Patent Information for CLRN1 gene:
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